Neural stimulation has been proposed as a therapy for a number of conditions. Neural stimulation may be delivered to modulate the autonomic system, which may be referred to as an autonomic modulation therapy (AMT). Examples of AMT include therapies for respiratory problems such as sleep disordered breathing, blood pressure control such as to treat hypertension, cardiac rhythm management, myocardial infarction and ischemia, heart failure (HF), epilepsy, depression, pain, migraines, eating disorders and obesity, and movement disorders. It has been proposed to deliver bursts of neural stimulation pulses synchronized to a cardiac cycle. However, it may be difficult to accurately sense cardiac activity during the AMT because, due to limitations in an implanted system, it can be technically challenging for the sensing circuitry to consistently detect cardiac activity while the therapy circuitry of the system is delivering a burst.